There are a bunch of options you might want to look at for document management and bookmarks. Check out the following:
- iUpload - Currently in use by several major banks, consulting firms, newspapers and one very large fast food giant. iUpload has blogs, wikis, tagging, access control and aggregation tools built in. Forrester ranked them the #1 enterprise blogging platform.
- Blogtronix - Similar enterprise features and they are working on developing their track record.
- Traction Software - Funded by the CIA, designed with security in mind, and currently used as a market intelligence tool.
- cyn.in - Very new, but interesting tool. Might not fit exactly with your required features, as it was designed as a work-place collaboration tool.
- WordPress MU - There is an open source version and a supported version. It is a great tool, but you might need some additional technical support to customize it to your needs.
- SocialText - This is an enterprise class wiki. It has an easy to use interface. SocialText has all the access control and audit trails you might need. However, to make it work in your environment, you will have to establish some user conventions. Think of how you would use Wikipedia to accomplish your goals. Make it technically much easier, and you have SocialText.
You can set up one off blogs and wikis using any number of tools, but what is missing with most of them (execpt the ones mentioned above) are the tools to manage large numbers of internal sites and internal users.
You might be interested in a white paper I wrote on the topic for more details.
The Next Wave in Productivity Tools - Web Office